LOCUS       NZ_CP058785             2058 bp    DNA     circular CON 02-MAY-2024
DEFINITION  Shigella flexneri strain STLIN_17 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP058785
VERSION     NZ_CP058785.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925572
            Assembly: GCF_022494355.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2058)
  AUTHORS   Che,Y., Xu,X., Yang,Y., Brinda,K., Hanage,W., Yang,C. and Zhang,T.
  TITLE     High-resolution genomic surveillance elucidates a multilayered
            hierarchical transfer of resistance between WWTP- and
            human/animal-associated bacteria
  JOURNAL   Microbiome 10 (1), 16 (2022)
   PUBMED   35078531
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2058)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUL-2020) Civil Engineering, The University of Hong
            Kong, Pokfulam Road, Hong Kong 000000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. Unicycler 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology :: Illumina; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022494355.1-RS_2024_05_02
            Annotation Date                   :: 05/02/2024 05:07:50
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,714
            CDSs (total)                      :: 4,591
            Genes (coding)                    :: 4,355
            CDSs (with protein)               :: 4,355
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 236
            CDSs (without protein)            :: 236
            Pseudo Genes (ambiguous residues) :: 0 of 236
            Pseudo Genes (frameshifted)       :: 70 of 236
            Pseudo Genes (incomplete)         :: 162 of 236
            Pseudo Genes (internal stop)      :: 43 of 236
            Pseudo Genes (multiple problems)  :: 38 of 236
            Pseudo Genes (short protein)      :: 3 of 236
            CRISPR Arrays                     :: 5
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058785.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..2058
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STLIN_17"
                     /isolation_source="Stanley WWTPs_17 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed5"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            159..1148
                     /locus_tag="HZT03_RS23425"
                     /old_locus_tag="HZT03_23245"
     CDS             159..1148
                     /locus_tag="HZT03_RS23425"
                     /old_locus_tag="HZT03_23245"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529700.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_040207214.1"
                     /translation="MQNPELQNLTDYSPSDAPWDAHRSVSDDVGGIYLLAAEYERYGAR
                     MASCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDSRWMFLTLTVRNCAIEELGETLSRMNTAFQRLKDRKEFRPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMVPPGMLNGKSYVRHERWVELWRECLRVSYDPNVDVRAVKPRKPKDG
                     ESLACATAELVRGAVAETLKYSTKPADMVADPKWFLELTRQTHKRRFVATGGALKDVLK
                     LDQETDADMVIGDDISEGDDDGSRIAFEWKTEVKKYRRSPTKDKTESD"
                     /name="protein rep"
     gene            1702..1893
                     /locus_tag="HZT03_RS23430"
                     /old_locus_tag="HZT03_23250"
     CDS             1702..1893
                     /locus_tag="HZT03_RS23430"
                     /old_locus_tag="HZT03_23250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020324555.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_020324555.1"
                     /translation="MIVRLDNRLFEILDEMGAHVDREMFMAAYAQRKAEKENDPRHIRQ
                     RKLTRLAHDLMSESDPEL"
                     /name="hypothetical protein"
     Typing          complement(875..1066)
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.446"
                     /coverage="100.0"
                     /evalue="2.86e-91"
ORIGIN
        1 ctgtcgggag tggtcgcaga aaaaagcgac ccccgcaact gcgctaacag ttcgggggtg
       61 tgaccacctg taggaattcg aatttggaca cgacaacaca ggtgatatgg caatgataac
      121 acgtcaaatg agccatcgcc cagcatgggg cggtgtgcat gcaaaatcct gaactccaga
      181 acctaactga ctactccccc tcagatgcgc cgtgggacgc tcacagaagc gtttctgacg
      241 acgtgggagg gatttacctg cttgcggctg aatatgagcg ctacggggcg cgtatggcct
      301 cctgtggcgg tttactgagg tttgggtggt ctaccctcaa agaaaccgga gaaacgcgcc
      361 tgaggctgcg tgaggcgcat ttctgccgtg tccggcactg tcctgtctgc cagtggaggc
      421 gctccctgat gtggcaagcc cgtttctacc agtccctgcc gcgtatcgtg gcggattacc
      481 ccgattcccg ctggatgttt ctgaccctga ccgtgcgcaa ctgcgcgatc gaggagctgg
      541 gcgagacgct gagccggatg aacacggctt tccagcgact gaaggaccgt aaagagttcc
      601 gaccagttca gggctggata cgcaccacgg aagtcacccg cggcagtgac ggcagcgcac
      661 acccgcactt ccacaccctg atgatggttc cgccgggcat gcttaacggg aagagttacg
      721 tcaggcatga acgctgggtt gagctgtggc gtgagtgcct gcgggtcagt tacgatccga
      781 atgtcgatgt ccgggcagtg aaaccccgca agccgaagga cggcgaatcg ctggcctgcg
      841 cgaccgccga actggtgcgc ggcgcagtgg ccgaaaccct gaaatattcc acgaagccgg
      901 ccgacatggt ggccgatcct aaatggttcc tcgaactgac ccgccagacg cacaagcgcc
      961 gctttgtggc gaccggcggc gcactcaaag acgtgctgaa actcgatcag gaaaccgacg
     1021 ccgacatggt gatcggggat gatatttccg agggcgatga tgacggttcc cgcatcgcgt
     1081 tcgagtggaa gaccgaggtc aaaaagtacc ggcgttcgcc gacgaaagat aaaaccgaat
     1141 cagactaaca gggtgtcggg gctgcgccct gaccatgagg gctttgggca tccgtcacct
     1201 tggtggcggt gtaccaaagt cacatcttgt ccgattgatt ttactccgat gcaggatagg
     1261 gctaacgccg caaagtgacg tcactcgatt actgagttcg gattccgaac ctgggttttt
     1321 cttccggtaa ttttccggaa ggcgcgctta gtagtttctc atctggcgat gagaaacgcg
     1381 cggtggggca agcccacgaa aaacaaaaac tgataacgga caagatgtgt ttttggagta
     1441 ccgccatcac gatgccggta ccaaaaacga tccgtcaggg ctgcgccccg acaccctgcc
     1501 aacacctcac gccgccagat taaaatctgt cagcgttcgc cgttcccgaa atcgtcaaac
     1561 gctaaatcgc ggggtcccgc tggcttgcca gtgggttccg atttagtgat tgacgacagc
     1621 acccgtaaaa tacttacagg gggtggttgt gatcacgcag tgagcgcaac cacctgataa
     1681 gcgttttttg agggggtagg catgatcgtc agactggata accggctgtt tgagattctc
     1741 gatgagatgg gtgcgcatgt ggatcgggaa atgttcatgg cggcctatgc gcagcggaag
     1801 gccgaaaaag aaaatgatcc ccggcatatc cgtcaacgga aactgaccag gttggctcat
     1861 gatttgatgt cagaatcgga ccctgaattg tgagcctcgc gtgcgcgcga gggaaatcgg
     1921 tcagaaaatg gccggagtct cgtgcgcgcg atccttgtat ttatacttaa gggataactc
     1981 tggcgtcaaa aaacgccgcc agcccttgtg ccgcaagggt ttgagtgtga tttgcctgaa
     2041 aatggttttg gaagtatt
//
